The problem I'm having is that the 'Export as PDF' menu item doesn't work exactly like "Print to PDF." The PDF output has almost zero margins, no header/footer to identify a source, and it's just not as desirable as printing-to-PDF from the print dialogue (though it is more efficient code-wise).

Can anyone here tweak the following script to produce the same result through the Print-to-PDF function? I gave it a shot but I'm new to AppleScript and couldn't get it to work. Thanks!

You might be able to re-use some of the code - look at the Keynote 5.3 version - as I recall that print dialog was the standard OS X print dialog as it would also appear in Safari....they customized it in Keynote 6.

It takes some patience and trial-and-error, but it's a task I had to do a couple times a day and it was worth it.

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Yeah, I just tested it and the Keynote 5.3 version works in Safari with one line (selecting Individual Slides in Keynote) commented out. Here's the script (I also deleted some if statements that would never be true in Safari, just to clean it up, and added your code to render in Reader):